Sounds like a business opportunity... Permanent marking paintballs...

True but maybe you can fill them yourself?

Filling paintballs is very hard and specialized and would probably be limiting to 99 out of 100 people if not more.

Gluing two fragile gelatin halves (designed to dissolve and break easily) once you’ve filled them perfectly full of paint and then making sure they’re almost perfectly round takes specialized equipment.

Syringe out the old paint, syringe in the new paint.